Hi Mete,
I am not sure it is the "sort" problem. I find "cufflinks" in galaxy is
unstable. I have bam files from Tophat which I can run cufflinks a few days
agao.

But these days when I run cufflinks with these bam files, the error shows.
Strangely, it can work some time. I don't know the reason.
ChenYao
2011/8/9 Jennifer Jackson <j...@bx.psu.edu>
> Hi Mete,
>
> This FAQ has a workflow for sorting a Bowtie (or any) SAM file for
> Cufflinks:
> http://main.g2.bx.psu.edu/u/**jeremy/p/transcriptome-**analysis-faq#faq2<http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2>
>
> Thanks!
>
> Jen
> Galaxy team
>
>
> On 8/4/11 10:27 AM, Mete Civelek wrote:
>
>> Hi,
>>
>> I'm trying to get read counts or FPKM values for my miRNA NGS data on
>> Galaxy. I have aligned the reads using Bowtie, but it appears that
>> Cufflinks gives an error when run on the Bowtie alignments (This might
>> have something to do with Bowtie's BAM file not being sorted). I know
>> that Tophat alignments work well with Cufflinks, but I'm not sure if it
>> would be possible to use Tophat for my data since miRNA don't have
>> splice junctions. I've tried without success to parameterize Tophat to
>> completely avoid assigning splice junctions (by setting the max intron
>> length to 1). Is there a way I can get the Bowtie alignment to work with
>> Cufflinks on Galaxy? Or perhaps there's a way I can parametrize Tophat
>> as to get no splice junctions?
>>
>> Thanks,
>>
>> Mete
>>
>>
>> ------------------------------**------------------------------**
>> ------------
>> IMPORTANT WARNING: This email (and any attachments) is only intended for
>> the use of the person or entity to which it is addressed, and may
>> contain information that is privileged and confidential. You, the
>> recipient, are obligated to maintain it in a safe, secure and
>> confidential manner. Unauthorized redisclosure or failure to maintain
>> confidentiality may subject you to federal and state penalties. If you
>> are not the intended recipient, please immediately notify us by return
>> email, and delete this message from your computer.
>>
>>
>> ______________________________**_____________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org. Please keep all replies on the list by
>> using "reply all" in your mail client. For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>>
>> http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>> http://lists.bx.psu.edu/
>>
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/**Support <http://galaxyproject.org/Support>
> ______________________________**_____________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>
> http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
>

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/